SUMMARY The Molecular Analysis of Genomic Instability Core will perform state-of-the-art assays for program investigators in the analyses of cytogenetic aberrations, and DNA damage responses and repair. These analyses will complement sequencing results (e.g., examine repetitive regions that are not covered by DNA sequencing approaches), and provide experimental validation for recurrent genomic instability and rearrangements identified using genomic approaches (Core C). In addition, the core will perform cell-based assays to detect and quantify biomarkers for DNA damage and DNA repair pathways, and measure DNA repair intermediates. Having a dedicated core for this program is beneficial: 1) for cost effectiveness and 2) for custom designing the experiments based on specific requirement for each of the projects. By centralizing these services under the leadership of two experienced investigators, Drs. Lorraine Symington and Shan Zha, the Core will enhance the productivity of the program project members by providing essential services to all projects, and ensure uniformity of data acquisition and interpretation. The core has two independent specific aims, which are built upon the expertise of the core leaders. The purpose of Aim 1 is to develop and perform cytogenetic assays to characterize chromosomal breaks, translocations and copy number changes by standard G-band karyotyping, spectral karyotyping (SKY), chromosomal painting and locus-specific FISH. In the second aim, the Core will provide services for automated imaging of DNA damage and response factors, and will apply quantitative PCR-based assays for detection of ssDNA formed by end resection of site-specific DSBs in yeast and mammalian cells, and DNA combing method to measure the length of resection tracks on single molecules from cells treated with irradiation or topoisomerase inhibitors.